Was meaning to say the following as a part of first email:

I understand, norm.factor calculated by edgeR considers information more
than library size. I understand the issue of limited "real estate" is
factored in as well. So, I assume, what is see may be okay. But, still
would like to get some second opinion for experts.

Thanks again,
Gowthaman

On Thu, Jun 21, 2012 at 4:07 PM, gowtham <ragowthaman@gmail.com> wrote:

> Hi Everyone,
> I am analyzing a RNAseq experiment with two groups each having two
> replicates. One out of 4 libraries have only half as much reads mapping to
> genome.
>
> Lib Fe+.1 has only 4 million reads while other are 9 million +. But still
> the norm.factors are not much different. With my naive understanding i
> expect Fe+.1 to be very different from others. I would like to know if what
> I see is okay?
>
> > oldsetDGE <- calcNormFactors(oldsetDGE)
> > oldsetDGE$samples
>       group lib.size norm.factors
> fe-.1     2  9664343    0.9865411
> fe-.2     2 11248827    1.0812947
> fe+.1     1  4194124    0.9662389
> fe+.2     1  9963626    0.9701888
>
>
> Thanks very much,
> Gowthaman
> --
> Gowthaman
>
> Bioinformatics Systems Programmer.
> SBRI, 307 West lake Ave N Suite 500
> Seattle, WA. 98109-5219
> Phone : LAB 206-256-7188 (direct).
>



-- 
Gowthaman

Bioinformatics Systems Programmer.
SBRI, 307 West lake Ave N Suite 500
Seattle, WA. 98109-5219
Phone : LAB 206-256-7188 (direct).

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